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In the Java perspective in Package Explorer, after removing a Source Folder or a Jar file that had been expanded with the + sign, the equivalent expansion will happen to the peer-level element that comes after it in the list. By "removing" a Jar or Source Folder, I mean that I went to the Project Properties and removed it from the Java Build Path area. It also happened when deleting a Jar file from the Project Explorer directly. This does not appear to happen when deleting plain directories, whether in the Java perspective or in the Resource perspective. However, plain directories do get expanded when an expanded Jar or Source Folder is removed that was before it in the list.
This is the known JFace tree expansion bug. Moving to platform UI.
*** This bug has been marked as a duplicate of 3840 ***